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Structure of Human BCCIP and Implications for Binding and Modification of Partner Proteins

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Structure of Human BCCIP and Implications for Binding and Modification of Partner Proteins bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 Structure of Human BCCIP and Implications for Binding and Modification of Partner Proteins Woo Suk Choi1, Bochao Liu2, Zhiyuan Shen2, Wei Yang1 1 Laboratory of Molecular Biology, NIDDK, National Institutes of Health, 9000 Rockville Pike, Building 5, Bethesda, MD 20892, USA 2 Rutgers Cancer Institute of New Jersey, Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, 195 Little Albany Street, New Brunswick, NJ 08901 Corresponding author: Wei Yang ([email protected]) Zhiyuan Shen ([email protected]) Running title: Crystal structure of human BCCIPb Keywords: BRCA2, tumor suppressor, ribosome biogenesis, acetyltransferase Abbreviations: 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 Abstract BCCIP was isolated based on its interactions with tumor suppressors BRCA2 and p21. Knockdown or knockout of BCCIP causes embryonic lethality in mice. BCCIP deficient cells exhibit impaired cell proliferation and chromosome instability. BCCIP also plays a key role in biogenesis of ribosome 60S subunits. BCCIP is conserved from yeast to humans, but it has no discernible sequence similarity to proteins of known structures. Here we report two crystal structures of an N-terminal truncated human BCCIPb, consisting of residues 61-314. Structurally BCCIP is similar to GCN5-related acetyltransferases (GNATs) but contains different sequence motifs. Moreover, both acetyl-CoA and substrate-binding grooves are altered in BCCIP. A large 19-residue flap over the putative CoA binding site adopts either an open or closed conformation in BCCIP. The substrate binding groove is significantly reduced in size and is positively charged despite the acidic isoelectric point of BCCIP. BCCIP has potential binding sites for partner proteins and may have enzymatic activity. 2 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 1 INTRODUCTION BCCIP is a nuclear protein that was identified in human genome based on its interactions with tumor suppressors BRCA2 and p21 1, 2. In humans, there are two isoforms resulting from alternative RNA splicing, BCCIPa (322 residues) and BCCIPb (314 residues), which share the identical N-terminal 258 residues but differ in the remaining C-terminal regions 1, 2. BCCIPa and b are also known as TOK-1a and TOK- 1b, respectively 1. BCCIPb is the conserved isoform in eukaryotes, from yeast, worms, plants to mammals 2, while BCCIPa only exists in humans. In mouse, there is only one BCCIP, which is ~70% identical to human BCCIPb. Either knockdown or knockout of BCCIP in mice leads to embryonic lethality due to impaired cell proliferation 3, 4. BCCIP deficient mouse embryo fibroblast cells exhibit increased sensitivity to DNA damage and replication stress and increased chromosome instability, including chromosome breaks and sister chromatid union 3. The yeast homolog of BCCIPb, known as BCP1, appears to be involved in nuclear export and ribosome biogenesis 5, 6. Recently, both mouse BCCIP and human BCCIPb were shown to be located in the nucleolus and required for rRNA maturation and ribosome 60S subunit biogenesis 7, but with distinct features from the yeast BCP1. Despite its functional importance, structures of BCCIP-family proteins remain elusive. Except for limited sequence similarity of ~50 residues to the Ca2+-binding domain in calmodulin and M-calpain 2, BCCIP has no discernible sequence homology to any known protein. Using isomorphous replacement we have determined crystal structures of a large fragment of human BCCIPb (aa 61-314) in two different crystal forms. To our 3 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 surprise, structurally BCCIP is homologous to the GCN5-related N-acetyltransferases (GNATs) 8, which use acetyl-CoA to modify primary amines of lysine sidechains or protein N termini, as well as aminoglycosides (antibiotics) and hormones (serotonin) 9-12. The regions corresponding to the substrate and catalytic motifs in N-acetyltransferases (motifs A-D), are also conserved among BCCIP-family members but are different from GNATs. Whether BCCIP is an enzyme, and what its substrates might be are unclear. While we were engaged in trying to figure out its structure-function relationship, a yeast BCP1 structure was reported earlier this year (with the structure coordinates on hold) 13. Here we present crystal structures of the conserved isoform of human BCCIPb and its outstanding binding surfaces for partner proteins and possibly for small molecules. 2 RESULTS AND DISCUSSION 2.1. Crystal structures of human BCCIP We have determined crystal structures of N-terminal truncated BCCIPb (aa 61-314, referred to as BCCIP hereafter) in two different space groups at resolutions of 3.06 (Native1) and 2.13 Å (Native2), respectively (Table 1). The two structures are superimposable except for a 19-residue extended and flexible loop. BCCIP forms a single domain of a/b fold, including a mixed seven-stranded b sheet surrounded on either side by four and three long a helices (Fig. 1). The structure can be divided into two halves. The N-terminal half (aa 61-185) folds into two baab hairpins with the four b strands (b1- b4) forming an antiparallel sheet, and four a helices forming two hairpins (aA-aB, and aC-aD) covering one face of the b sheet. Helix aC is preceded by a short helix aC’ 4 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 (aa132-136). The C-terminal half (aa 186-314) folds in the order of ababba and forms a three-stranded antiparallel b sheet (b5-7), with three a helices (aE-aG) on the side opposite to helices aA-aD (Fig. 1a-b). The two halves are linked by helix aE and form a contiguous b sheet by hydrogen bonds at the beginning of parallel strands b4 and b5. These two strands diverge at the end giving the b sheet a V shape (Fig. 1b). No Ca2+- binding module or metal ion-binding site can be found. The extended loop linking b6 and b7, L67 (aa 269-287), has two dramatically different conformations. In Native1 L67 is extended and interacts with a crystallographic symmetry mate reciprocally. But in Native2 L67 is folded next to aA-aB, and L67 and aAB are like two arms embracing the b sheet (Fig. 1b). The N-terminal half followed by aE and b5 has the same sequence in the two isoforms of human BCCIP, and only aF-b6-b7-aG differ between the two. 2.2. BCCIP is structurally similar to GNAT acetyltransferases Structural similarity search by Dali revealed that BCCIP is similar to GCN5-related acetyltransferases (GNATs), with substrates ranging from histones to antibiotics and hormones. The N-terminal half of BCCIP is superimposable with these GNATs (Fig. 2a). But in GNATs helices aC and aD are absent and b3 and b4 are linked by a b hairpin directly or a random coil 9-12, 14. Helices aC and aD effectively close the open binding groove for protein substrates, such as the histone tail bound to GCN5 14, and fill it with hydrophobic residues. With its positively charged pocket (Fig. 1c) BCCIP may still be able to bind small molecules, such as antibiotics and hormones. 5 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416925; this version posted December 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Choi et al., 2020 The structurally most conserved region (motifs A and B) involving in acetyl-CoA binding in GNATs is located between two halves of the structure at b4-b5 8. The corresponding region is also conserved among BCCIP-family members, but the sequence motifs of BCCIP (Fig. 1b) differ from GNATs 15. The C-terminal half of BCCIP is oriented differently from GNATs, particularly loop L5F, which binds the diphosphates of CoA in GNATs. BCCIP contains an insertion in L5F, and without structural changes, its L5F would clash with the CoA moiety Fig. 2b). In case substrate binding induces conformational changes in BCCIP, we tried co-crystallization of BCCIP with 10 different acyl-CoA compounds. Instead of finding a bound substrate, we obtained a different form of apo BCCIP crystal (Native2) (see section 3.2). In addition, compared to GNATs, BCCIP has the following two insertions, the extended flexible loop L67, which is open and extended in Native1 and adopts a closed conformation in Native2 (Fig. 2c), and the C-terminal helix aG. Together with L5F, these insertions alter the acetyl-CoA binding site significantly. Peculiarly, two Tyr residues, Y64 and Y71, are exposed 2.3. Potential binding surface for protein and small molecules The conserved residues among BCCIP homologs are clustered into two groups.
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